A simple tool extends TIMSTOF compatibility with historic data processing tools and enables ion mobility-enhanced spectral libraries

Trapped ion mobility mass spectrometry is proving to be a disruptive technology in LCMS based proteomics. One primary drawback of this hardware is the lack of compatibility with the hundreds of data processing pipelines historically in use. This study describes a simple data conversion tool that folds the TIMSTOF ion mobility data into the MS2 fragmentation spectra allowing simple downstream processing. Little to no detriment in the assignment of peptide spectral matches is observed when folding the 1/k0 value into the low mass region. To demonstrate one utility of TIMS Folding, spectral libraries are provided in multiple common formats that were constructed from the same files both with and without folded ion mobility data. When new data is acquired and folded using the same parameters prior to data processing the folded ion mobility data can be used as an additional metric for peptide match confidence against folded spectral libraries.

The Study of Stress Conditions on Growth and Proteome of Raoultella Planticola: A New Emerging Pathogen

All bacteria can survive and adapt to different stresses such as fluctuations in temperature, pH oxidative, and osmotic pressure occurring in their surrounding environments. This study aims to evaluate the effects of a variety of stress conditions on the growth, and proteome of Raoultella planticola PTCC 1598. R. planticola cells were exposed to different values of temperatures, sodium chloride, pH, and hydrogen peroxide stresses. Amongst the stress conditions, oxidative stress upon exposure to hydrogen peroxide (H2O2) at 4000 ppm concentration was selected for proteomics analysis in detail. Approximately 1400 spots were identified in two-dimensional gel electrophoresis (2-DE). Among the identified spots, 85 spots were repeatable using 2D-Platinum software and eye confirmation and, nine protein spots were differentially expressed. Among nine proteins, six proteins identified successfully with a MASCOT score greater than 40 (p<0.05) were 2, 3-dihydroxybenzoate-2, 3-dehydrogenase (oxidoreductase family), D-galactose-binding periplasmic protein, uridine phosphorylase (glycosyltransferases), uridine phosphorylase, a single peptide match to cysteine-binding periplasmic protein, and NADP(H) nitroreductase. All identified proteins showed decreased level expression. Based on the obtained results, we concluded that hydrogen peroxide as an antiseptic compound could affect cell growth and proteomics of R.planticola. So, we recommend using an antiseptic solution containing H2O2 to prevent the spread of R.planticola as a new emerging pathogen.

Oligopeptides for Immunotherapy Approaches in Ovarian Cancer Treatment

Background: Anti-ovarian cancer vaccines based on minimal immune determinants uniquely expressed in ovarian cancer biomarkers appear to promise a high level of sensitivity and specificity for ovarian cancer immunodiagnostics, immunoprevention, and immunotherapy. Methods: Using the Pir Peptide Match program, three ovarian cancer biomarkers – namely, sperm surface protein Sp17, WAP four-disulfide core domain protein 2, and müllerian-inhibiting substance – were searched for unique peptide segments not shared with other human proteins. Then, the unique peptide segments were assembled to define oligopeptides potentially usable as synthetic ovarian cancer antigens. Results and Conclusion: This study describes a methodology for constructing ovarian cancer biomarkerderived oligopeptide constructs that might induce powerful, specific, and non-crossreactive immune responses against ovarian cancer.

Identification of best indicators of peptide-spectrum match using a permutation resampling approach

Various indicators of observed-theoretical spectrum matches were compared and the resulting statistical significance was characterized using permutation resampling. Novel decoy databases built by resampling the terminal positions of peptide sequences were evaluated to identify the conditions for accurate computation of peptide match significance levels. The methodology was tested on real and manually curated tandem mass spectra from peptides across a wide range of sizes. Spectra match indicators from complementary database search programs were profiled and optimal indicators were identified. The combination of the optimal indicator and permuted decoy databases improved the calculation of the peptide match significance compared to the approaches currently implemented in the database search programs that rely on distributional assumptions. Permutation tests using p-values obtained from software-dependent matching scores and E-values outperformed permutation tests using all other indicators. The higher overlap in matches between the database search programs when using end permutation compared to existing approaches confirmed the superiority of the end permutation method to identify peptides. The combination of effective match indicators and the end permutation method is recommended for accurate detection of peptides.